Manufacturable sub-3 nanometer palladium gap devices for fixed electrode tunneling recognition

ABSTRACT

A technique is provided for manufacturing a nanogap in a nanodevice. An oxide is disposed on a wafer. A nanowire is disposed on the oxide. A helium ion beam is applied to cut the nanowire into a first nanowire part and a second nanowire part which forms the nanogap in the nanodevice. Applying the helium ion beam to cut the nanogap forms a signature of nanowire material in proximity to at least one opening of the nanogap.

BACKGROUND

The present invention relates generally to nanodevices, and morespecifically, to manufacturing a sub-3 nanometer palladium nanogap.

Nanopore sequencing is a method for determining the order in whichnucleotides occur on a strand of deoxyribonucleic acid (DNA). A nanopore(also referred to as pore, nanochannel, hole, etc.) can be a small holein the order of several nanometers in internal diameter. The theorybehind nanopore sequencing is about what occurs when the nanopore issubmerged in a conducting fluid and an electric potential (voltage) isapplied across the nanopore. Under these conditions, a slight electriccurrent due to conduction of ions through the nanopore can be measured,and the amount of current is very sensitive to the size and shape of thenanopore. If single bases or strands of DNA pass (or part of the DNAmolecule passes) through the nanopore, this can create a change in themagnitude of the current through the nanopore. Other electrical oroptical sensors can also be positioned around the nanopore so that DNAbases can be differentiated while the DNA passes through the nanopore.

The DNA can be driven through the nanopore by using various methods, sothat the DNA might eventually pass through the nanopore. The scale ofthe nanopore can have the effect that the DNA may be forced through thehole as a long string, one base at a time, like thread through the eyeof a needle. Recently, there has been growing interest in applyingnanopores as sensors for rapid analysis of biomolecules such asdeoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, etc.Special emphasis has been given to applications of nanopores for DNAsequencing, as this technology holds the promise to reduce the cost ofsequencing below $1000/human genome.

SUMMARY

According to one embodiment, a method for manufacturing a nanogap in ananodevice is provided. The method includes disposing an oxide on awafer, disposing a nanowire on the oxide, and applying a helium ion beamto cut the nanowire into a first nanowire part and a second nanowirepart to form the nanogap in the nanodevice. Applying the helium ion beamto cut the nanogap forms a signature of nanowire material in proximityto at least one opening of the nanogap.

According to one embodiment, a method for manufacturing a nanogap in ananodevice is provided. The method includes disposing an oxide on awafer, disposing a nanowire on the oxide, and applying a helium ion beamto taper the nanowire laterally into a first nanowire part and a secondnanowire part. The first nanowire part and the second nanowire part forma first nanogap in the nanodevice. Applying the helium ion beam to taperthe nanowire laterally forms a bridge connecting the first nanowire partand the second nanowire part. A second nanogap is cut in the bridge toform a first extension from the first nanowire part and form a secondextension from the second nanowire part.

According to one embodiment, a structure utilized in sequencing. Thestructure includes an oxide on a wafer, a nanowire on the oxide, and atapered lateral area of the nanowire from applying a helium ion beam.The tapered lateral area forms a first nanowire part and a secondnanowire part, and the first nanowire part and the second nanowire partform a first nanogap. The tapered lateral area forms a bridge connectingthe first nanowire part and the second nanowire part. A second nanogapin the bridge forms a first extension from the first nanowire part andforms a second extension from the second nanowire part.

Additional features and advantages are realized through the techniquesof the present invention. Other embodiments and aspects of the inventionare described in detail herein and are considered a part of the claimedinvention. For a better understanding of the invention with theadvantages and the features, refer to the description and to thedrawings.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The subject matter which is regarded as the invention is particularlypointed out and distinctly claimed in the claims at the conclusion ofthe specification. The forgoing and other features, and advantages ofthe invention are apparent from the following detailed description takenin conjunction with the accompanying drawings in which:

FIG. 1A illustrates a cross-sectional view of a method of forming ananodevice according to an embodiment.

FIG. 1B illustrates a top view of the nanodevice according to anembodiment.

FIG. 1C illustrates a cross-sectional view of a nanogap cut in ananowire according to an embodiment.

FIG. 1D illustrates a top view of the nanogap in the nanodeviceaccording to an embodiment.

FIG. 2A is a picture via a transmission electron microscope (TEM) of ananowire according to an embodiment.

FIG. 2B is a TEM picture of a first nanogap cut by a helium ion beamunder certain conditions according to an embodiment.

FIG. 2C is a TEM picture of a second nanogap cut by a helium ion beamunder certain conditions according to an embodiment.

FIG. 2D is a TEM picture of a third nanogap cut by a helium ion beamunder certain conditions according to an embodiment.

FIG. 2E is a TEM picture of a unique signature surrounding the nanogapaccording to embodiment.

FIG. 2F is a TEM picture of the nanogap with residual palladiumaccording to an embodiment.

FIG. 2G is a TEM picture of the nanogap with the residual palladiumremoved according to an embodiment.

FIG. 3A schematically illustrates an array of nanodevices each having ananogap formed by the helium ion beam according to embodiments.

FIG. 3B schematically illustrates testing each individual nanodevice inthe array to determine whether residual palladium is in the nanogapaccording to embodiments.

FIG. 4A illustrates a top view of the nanodevice in which the nanowireis intentionally tapered by the helium ion beam according to anembodiment.

FIG. 4B illustrates a top view of the nanodevice with left and rightextensions respectively extending from left and right electrodes to forma second nanogap according to an embodiment.

FIG. 4C illustrates an enlarged, partial top view of the nanodeviceshowing a bridge according to an embodiment.

FIG. 4D illustrates the enlarged, partial top view of the nanodevice inwhich the bridge is cut forming the two extensions according to anembodiment.

FIG. 4E illustrates another enlarged, partial top view of the nanodevicewith the two extensions according to an embodiment.

FIG. 5A illustrates a sequencing system utilizing the nanodeviceaccording to an embodiment.

FIG. 5B illustrates an enlarged, partial view of the system showings thetwo extensions according to an embodiment.

FIG. 6 is a flow diagram illustrating a method for manufacturing ananogap of the nanodevice in the nanowire according to an embodiment.

FIG. 7 is a flow diagram illustrating a method for manufacturingnanogaps in the nanowire of the nanodevice according to an embodiment.

FIG. 8 is a block diagram that illustrates an example of a computer(computer test setup) having capabilities, which may be included inand/or combined with embodiments.

DETAILED DESCRIPTION

The fabrication of a sub-3 nm gap between two palladium electrodes hasbeen pursued to create a device capable of recognizing individual DNAbases by tunneling current measurements. This base recognition device isthe key component of generation 4 single molecule sequencing technology.Towards this end, several approaches have been proposed or pursued toachieve a sub-3 nm gap between electrodes, such as a focusedtransmission electron microscope (TEM) beam cutting, or scanningtunneling microscope electrodes. The primary problem with all of thesesolutions is that none of them provides a clear cut path to scaling up(manufacturing) production of the tunneling devices. Reproducibility orconsistency of the nanogaps at these dimensions has also been achallenge. Importantly, manufacturing approaches commonly used toachieve high-fidelity nanoscale features like electron beam (e-beam)lithography can be inadequate to realize the needed gap sizes.

Embodiments are configured to use a focused helium beam to mill throughpalladium (Pd) nanowires to fabricate sub-3 nm gap devices for DNA baserecognition. Dividing a continuous palladium nanowire in this way tocreate two separate palladium electrodes provides a high throughput andreproducible path for sub-3 nm gap creation with a unique andidentifiable process signature. The focused helium beam method alsopermits tapering of the nanowire to enhance tunneling recognitioncapabilities. For example, the electrodes can be sharpened to a finertip closer to the gap to reduce the probability of tunneling signaturesoriginating from multiple bases simultaneously. In addition, the heliumbeam cutting method can be applied to any substrate in contrast to theTEM approach, which is confined to globally or locally thin substrates.

FIG. 1A illustrates a cross-sectional view of a method of forming ananogap in a nanodevice 100 according to an embodiment. The nanodevice100 has an electrically insulating substrate 102 which may be a siliconwafer. An oxide layer 104 may be deposited (e.g., grown) on thesubstrate 102. The oxide layer 104 is a dielectric material, and may beany dielectric material including silicon dioxide.

A nanowire 106 is deposited on the oxide layer 104. FIG. 1B illustratesa top view of the nanodevice 100. The material of the nanowire may bepalladium. The palladium nanowires 106 can be fabricated on thedielectric oxide layer 104 using, for example, e-beam lithography andlift-off. The nanowires 106 can also be defined by optical lithographyand reactive ion etching. The width W of the nanowires 106 may rangefrom a few nanometers to micrometers (e.g., 3 nm to 8 μm) and thethickness T may vary from 2 nm to 50 nm.

With the palladium nanowire 106 in place, a helium ion microscope 120with a focused He ion beam is used to controllably create sub-3 nm gapsby varying the exposure conditions. FIG. 1C illustrates across-sectional view of a sub-3 nm nanogap 110 cut in the nanowire 106,while FIG. 1D illustrates a top view of the nanogap 110. The cutting bythe helium microscope 120 results in palladium electrode 106A (e.g.,left nanowire electrode) and palladium electrode 106B (e.g., rightnanowire electrode) which together form the nanowire 106. The width ofthe nanogap 110 is shown by D1. The width D1 of the nanogap 110 isformed to be less than 3 nanometers (e.g., 1 or 2 nm) via He ionsirradiated from the helium ion microscope 120. Similar to an electronmicroscope, one skilled in the art understands the operation of thehelium ion microscope 120 at discussed herein.

An example of commercially available helium ion microscopes are theORION™ Helium ion Microscope from Carl Zeiss SMT and the Multiple IonBeam Microscopes from Carl Zeiss SMT.

The following example shows the gap cutting conditions of the helium ionmicroscope 120 for palladium nanowires 106 with specific dimensions inwhich the width is approximately (˜) 20 nm and the thickness isapproximately 10 nm (where the thickness is 1 nm Ti and 9 nm Pd). In theexample exposure conditions (to control the helium ion microscope 120),the beam current is 0.4 pA (picoamperes), the beam spot size is 3.4 to 5Å (angstroms), the step size is 5 Å, the working distance may be 7.354mm (millimeters), and the aperture (opening) is 5 μm.

By varying parameters (in the helium ion microscope 120) such as theexposure time per pixel, a nanogap can be reproducibly fabricated with adistance (D1) less than 3 nm. At 30 kV (kilovolts), 2 μs/pixel (exposuretime) on a 15 nm wide and 10 nm thick palladium nanowire (line) in FIG.2A yields a 4 nm gap (e.g., nanogap_1) in FIG. 2B. By reducing theexposure time per pixel, the width of the gap can be made smaller. Inthis case, a 1 μs/pixel exposure time generates a 3 nm gap (nanogap_2)shown in FIG. 2C, and 0.5 μs/pixel exposure time generates a gap(nanogap_3) (e.g., between 1 and 3 nm) that is below the resolution ofthe helium microscope shown in FIG. 2D.

Note that in FIGS. 2A, 2B, 2C, and 2D (along with FIGS. 2E through 2G)the evaporated palladium lines (i.e., nanowires 106) are cut by afocused helium beam, and the resulting gaps are respectively shown bythe arrows pointing to nanogap_1, nanogap_2, and nanogap_3. FIG. 2Ereveals electrode nanogaps of less than 3 nm (e.g., 2.77 nm). Also, asseen in FIG. 2E, use of the helium ion beam provides a unique signatureaccording to an embodiment. Note the (unique) signature splash ofpalladium particles/dots 205 surrounding the nanogap is a result of Heion beam exposure according to embodiments. The palladium dots 205 mayhave sizes ranging from 2 to 8 nm in diameter. The palladium dots 205surrounding the nanogap 110 are not observed with TEM cutting on thinmembranes (i.e., thin electrodes).

FIG. 2F shows one palladium gap with residual palladium 210 stillconnecting (i.e., bridging) the electrodes 106A and 106B after cuttingwith the helium ion beam. In this case, the focusing of the electronbeam in the TEM (or He ion beam) is used to remove the residualpalladium 210 yielding the nanogap 110 shown in FIG. 2G. The nanogap 110is 2.97 nm. The structures in FIGS. 2A through 2G were imaged with highresolution transmission electron microscopy (TEM).

FIG. 3A illustrates an array of nanodevices 100 each having a nanogap110 formed by the helium ion beam of the helium ion microscope 120according to embodiments. FIG. 3B illustrates how each individualnanodevice 100 may be tested to determine if there is residual palladiumdot/particle 205 in the gap 110 between electrodes 106A and 106B.Voltage of voltage source 310 is applied to the electrodes 106A and 106Bto generate a current measured by an ammeter 315, and the amount ofcurrent determines if there is a residual palladium particle 205 in thegap 110. Assume that there is a residual particle 205A bridging (i.e.,physically and/or electrically connecting) the electrode 106A toelectrode 106B, and in such a case, the measured current by ammeter 315may be nanoamperes to microamperes because of the residual particle205A. If no residual particle 205A is present (in gap 110) betweenelectrode 106A and electrode 106B, the measured current may be in therange of 200 pA at 400 mV bias.

When it is determined during manufacturing that residual particles 205Aare connecting the two electrodes 106A and 106B, there are two options.The occasional nanodevices 100 having the residual particles 205A in thegap 110 may be discarded, while the remaining nanodevices 100 in thearray on the wafer 102 are utilized for sequencing as discussed herein.Alternatively and/or additionally, the nanodevices 100 having theresidual particle 205A may be further treated with an electron beam of atransmission electron microscope (and/or He ion beam) in the gap 110 toclear the residual particle 205A. Removing the residual particle 205Awith the electron beam results in the clear nanogap 110 shown in FIGS.1C and 1D. Out of the array of nanodevices 100 on the wafer 102, theremay be only a few nanodevices 100 that have the residual particle 205Aremaining in the gap 110, and the residual particle 205A is cut(removed) by the electron beam of the transmission electron microscopeeven though the gap 110 has already been (originally) cut using thehelium ion beam of the helium ion microscope 120.

Cutting a sub-3 nm gap with an electron beam (from start to finish)requires an enormous amount of time and skill as compared with a heliumion beam. Therefore, even if a few (e.g., 15%) out of an array ofnanodevices 100 on wafer 102 have a residual particle 205A in the gap110 (originally cut by the helium ion beam), the time to then remove theresidual particle 205A using the electron beam (for the few nanodevices100) is much less than the time required to cut gaps for an array ofnanodevices using the electron beam. TEM requires sample mounting (i.e.,nanodevice 100 mounting) and high vacuum which takes up to 30 minutes(min) for any given sample inserted in the TEM. Then, each gap takesabout 20 min to cut exclusively by TEM. The TEM touch up of previouslyHe beam cut gaps only requires a few milliseconds of beam exposure toremove residual Pd (e.g., from the nanogap 110).

FIG. 4A illustrates a top view of the nanodevice 100 in which thenanowire 106 has been intentionally tapered by the He ion beam in thevicinity of the nanogap 112 according to an embodiment. The helium ionmicroscope 120 is controlled to cut the nanowire laterally on side A andside B without cutting completely through the nanowire 106. Thisintentionally leaves a palladium bridge 405 connecting the leftelectrode 106A to the right electrode 106B. The nanogap 112 is cut witha width D2 that is larger than the width D1.

The helium ion microscope 120 (and/or an electron microscope) iscontrolled to cut a smaller nanogap 114 in the palladium bridge 405resulting in extension 405A and extension 405B in FIG. 4B. FIG. 4Billustrates a top view of the nanodevice 100 with left extension 405Aextending from and as part of electrode 106A, and with right extension405B extending from and as part of electrode 106B. The newly formednanogap 114 has a width that may equal and/or be less than the width D1of nanogap 110. The width D2 of the nanogap 112 may be 4 to 10 nm andthe width of the smaller nanogap D3 (formed between extensions 405A and405B) may be, e.g., 0.3, 0.4, 0.5, 0.7, . . . 1 through 2 nm (tofit/accommodate the diameter (size) base/nucleotide to be sequenced). Byhaving a larger nanogap 112 (D2) during DNA sequencing, the largernanogap 112 ensures that multiple DNA bases are not interacting with theelectrodes 106A and 106B because the distance (D2) between theelectrodes 106A and 106B (e.g., 7 nm or more) is too large for tunnelingcurrent to travel. As understood by one skilled in the art, the DNA ismoved into nanogap 114 between the extensions 405A and 405B (of therespective electrodes 106A and 106B). The dimension X of the extensions405A and 405B may be made to accommodate a single base in the nanogap114. For example, the dimension X has a distance smaller than theseparation/spacing between bases of the molecule being tested. Thedistance X of the extensions 405A and 405B may be 3, 4, 5, 6, 7angstroms depending on (base separation distance of) the target moleculebeing sequenced. Therefore, if the distance X is 3.5 Å, the nanogap 114between extensions 405A and 405B can (only) have a single base at a timeand the measured tunneling current can identify the particular basepresently in the nanogap 114 without simultaneously measuring tunnelingcurrent from neighboring bases that may be in the larger nanogap 112.The dimension X1 of the nanowire 106 may be 20.

In FIGS. 4A and 4B, view 410 is a dashed circle of an enlarged portionshown in FIGS. 4C, 4D, and 4E. The views 410 in FIGS. 4C, 4D, and 4E arepartial views; the substrate 102 and oxide 104 are not shown so as notto obscure the figures.

FIG. 4C illustrates a partial top view of the nanodevice 100 in whichthe palladium bridge 405 is shown as rounded portions (physically andelectrically) connecting the left and right electrodes 106A and 106B inthe nanogap 112. FIG. 4D illustrates the partial top view of thenanodevice 100 in which the palladium bridge 405 has been further cut(via the helium ion beam and/or electron beam of the helium ionmicroscope 120) into the two separate extensions 405A and 405B (shown asrounded portions extending from electrodes 106A and 106B). This resultsin the smaller nanogap 114 only between extensions 405A and 405B.

FIG. 4E illustrates the partial top view of the nanodevice 100 in whichthe two extensions 405A and 405B are shown as triangular shaped portionsextending from electrodes 106A and 106B according to an embodiment. Thenanogap 114 is between the triangular shaped portions.

FIG. 5A illustrates a system 500 for sequencing using the nanodevice 100according to an embodiment. As discussed above, the nanodevice 100includes the electrically insulating substrate 102 (wafer), oxide 104,electrodes 106A and 106B (with respective extensions 405A and 405B notshown for the sake of clarity), and nanogap 110 (or nanogaps 112 and114).

The system includes electrically insulating films 503 and 506. Abackside cavity 504 forms a suspended membrane making up the nanogap 110(nanogap 112 and 114). The electrodes 507 and 508 are metal contactpads, which may be any metal.

In the system 500, a top reservoir 514 is attached and sealed to the topof the insulating film 506, and a bottom reservoir 515 is attached andsealed to the bottom of the insulating film 503. Electrode 512 is in thetop reservoir 514, and electrode 513 is in the bottom reservoir 515.Electrodes 512 and 513 may be silver/silver chloride, or platinum forexample. The reservoirs 514 and 515 are the inlet and outletrespectively for buffer solution 550, and reservoirs 514 and 515 holdthe DNA and/or RNA samples for sequencing. The buffer solution 550 is anelectrically conductive solution (such as an electrolyte) and may be asalt solution such as NaCl.

The system 500 shows a target molecule 511, which is the molecule beinganalyzed and/or sequenced. As an example DNA sample, the system 500 mayinclude a single stranded DNA molecule 511, which is passing through thenanogap 110 (nanogaps 112 and 114). The DNA molecule 511 has bases 530(A, G, C, and T) represented as blocks.

The DNA molecule 511 is pulled through the nanogap 110 (nanogaps 112 and114) by a vertical electrical field generated by the voltage source 517.When voltage is applied to electrodes 512 and 513 by the voltage source517, the voltage generates the electric field (between reservoirs 514and 515) that controllably (e.g., by turning on and off the voltagesource 517) drives the DNA molecule 511 into and through the nanogap 110(nanogaps 112 and 114). Also, the voltage of the voltage source 517 canproduce the gate bias between electrodes 507 and 508. Note that theelectrodes 507, 508, 106A, and 106B, nanogap 110 (114) may operate as atransistor. The voltage across the nanogap 110 (nanogaps 112 and 114)from the voltage source 517 can be the gate for controlling thetransistor. Metal pads (electrodes) 507 and 508 are the drain and sourcerespectively for the transistor device. Voltage applied by voltagesource 519 to electrodes 507 and 508 also builds the electrical field,which can hold the base 530 in the nanogap 110 for sequencing. Note thatmetal pads 507 and 508 are electrically connected to electrodes 106A and106B having the nanogap 110 (nanogaps 112 and 114).

Note that a nanopore 580 is formed in layers 506 and 104 which is largerthan the nanogap 110 (112 and 114). The nanogap 110 (112 and 114) is inthe nanopore 580. The nanopore 580 connects top reservoir 514 to bottomreservoir 515 as understood by one skilled in the art. Ammeter 518monitors the ionic current change when DNA (or RNA) molecule 511 goesthrough nanogap 110 (112 and 114) (which is within the nanopore 580).The ionic current (measured by the ammeter 518) flows through electrode512, into the buffer solution 550, through the nanopore 580 (to interactwith the base 530 when the target molecule 511 is present in thenanopore 580), out through the electrode 513. Voltage generated by thevoltage source 519 produces the voltage between source 508 and drain507. Another ammeter 520 monitors the source-drain transistor currentfrom nanogap 110 (112 and 114) (of the transistor through the buffersolution 550) to detect nucleotide (i.e., base) information when theDNA/RNA molecule 511 passes through the nanogap 110 (112 and 114).

For example, when a base 530 is in the nanopore 580 (between the nanogap110 (or nanogaps 112 and 114) of the nanowire 106) and when voltage isapplied by the voltage source 519, source-drain transistor current flowsto source 508, into the right nanowire electrode 106B, into the buffersolution 550 (between the nanogap) to interact with the base 530positioned therein, into left nanowire electrode 106A, out through thedrain 507, and to the ammeter 520. The ammeter 520 is configured tomeasure the change in source-drain current when each type of base 530 ispresent in the nanogap 110 (nanogaps 112 and 114) (between the left andright electrodes 106A and 106B) and also when no base 530 (of the DNAmolecule 511) is present. The respective bases 530 are determined by theamplitude of the source-drain transistor current when each respectivebase in present in the nanogap 110 (or nanogaps 112 and 114) of thenanopore 580. As discussed for FIGS. 4B, 4D, and 4E, FIG. 5B illustratesa partial view of the system 500 with extensions 405A and 405B extendingfrom electrodes 106A and 106B respectively. The single base is (only)within the nanogap 114 although other bases 530 may be in the largernanogap 112.

When the single base 530 is present in the nanogap 114 and when voltageis applied by the voltage source 519, source-drain transistor currentflows to source 508, into the right nanowire electrode 106B, into rightextension 405B, into the buffer solution 550 (between the nanogap 114)to interact with the base 530 positioned therein, into left extension405A, into left nanowire electrode 106A, out through the drain 507, andto the ammeter 520. The ammeter 520 is measure the tunneling current(source-drain current) when the base 530 is present in the nanogap 114.This same process occurs for the rectangular and triangular shapedextensions 405A and 405B shown in FIGS. 4B and 4E.

FIG. 6 illustrates a method for manufacturing a nanogap in the nanowire106 (of the nanodevice 100) which can be utilized for DNA, RNAsequencing according to an embodiment. Reference can be made to FIGS.1-5 discussed herein.

An oxide 104 is disposed (e.g., grown) on top of a substrate 102 (wafer)at block 605, and the nanowire 106 is disposed on top of the oxide 104at block 610. The lift-off process may be utilized to dispose andpattern the metal of the nanowire 106. As understood by one skilled inthe art a positive resist process or a negative resist process may beutilized to dispose and pattern the nanowire 106.

A helium ion beam is applied via the helium ion microscope 120 to cutthe nanowire 106 into a first nanowire part (e.g., electrode 106A) and asecond nanowire part (e.g., electrode 106B) to form the nanogap 110 inthe nanodevice 100 at block 615.

When the helium ion beam is applied (via the helium ion microscope 120)to cut the nanogap 110, a signature of nanowire material (e.g.,palladium particles/dots 205) is formed in the proximity to the openingsof the nanogap 110 (e.g., as shown in FIGS. 2E and 3B) at block 620.

The signature of the nanowire material comprises nanowire materialparticles (e.g., palladium particles/dots 205) in proximity to theopenings of the nanogap 110 as a result of the helium ion beam. The Hebeam energy vaporizes the palladium which may redeposit in rounddroplets when the He beam is switched off.

As a result of applying the helium ion beam, voltage is applied by thevoltage source 310 to determine that a nanowire material particle (i.e.,palladium particle 205A) is lodged in the nanogap 110 in which thenanowire material particle connects the first nanowire part and thesecond nanowire part (i.e., connects electrode 106A to electrode 106B).When it is determined that the nanowire material particle is lodged inthe nanogap 110, the nanowire material particle in the nanogap 110 isremoved by applying an electron beam and/or a helium ion beam. Note thatthe helium ion microscope 120 may be configured to irradiate bothelectron beams and helium ion beams as desired. Alternatively and/oradditionally, when it is determined that the nanowire material particleis lodged in the nanogap 110, the particular nanodevice 100 having thenanowire particle lodged in the nanogap 110 out of an array of goodnanodevices 100 (shown in FIG. 3A) having nanogaps 110 (with no lodgedpalladium particles 205 as determined in FIG. 3B).

The nanowire 106 may be (only) palladium and/or other metals. Thesubstrate/wafer 102 may be silicon, germanium, etc. The oxide 104 may besilicon dioxide, and/or other dielectric materials.

FIG. 7 illustrates a method for manufacturing nanogaps 112 and 114(which may be the same as nanogap 110) in the nanowire 106 (of thenanodevice 100) which can be utilized for DNA, RNA sequencing accordingto an embodiment. Reference can be made to FIGS. 1-5 discussed herein.

An oxide 104 is disposed (e.g., grown) on top of a substrate 102 (wafer)at block 705, and the nanowire 106 is disposed on top of the oxide 104at block 710. The lift-off process may be utilized to dispose andpattern the metal of the nanowire 106. As understood by one skilled inthe art a positive resist process or a negative resist process may beutilized to dispose and pattern the nanowire 106.

A helium ion beam is applied via the helium ion microscope 120 to taperthe nanowire 106 laterally (e.g., on side A and side B but not inbetween) into a first nanowire part (e.g., electrode 106A in FIG. 4A)and a second nanowire part (e.g., electrode 106B), where the firstnanowire part and the second nanowire part form a first nanogap (e.g.,nanogap 112) in the nanodevice 100 at block 715.

Applying the helium ion beam to taper the nanowire laterallyintentionally forms a bridge 405 connecting the first nanowire part(electrode 106A) and the second nanowire part (electrode 106B) at block720.

Further applying the helium ion beam and/or an electron beam cut asecond nanogap (e.g., nanogap 114) in/through the bridge 405 to form afirst extension (e.g., extension 405A) from/on the first nanowire part(electrode 106A) and form a second extension (e.g., extension 405B)from/on the second nanowire part (electrode 106B) at block 725.

The second nanogap 114 is thinner than the first nanogap 112 (i.e.,D3<D2). The nanowire 106 is tapered in order for the first extension405A and the second extension 405B to have rectangular shapes after thesecond nanogap 114 is cut as shown in FIGS. 4A and 4B. The nanowire 106is tapered in order for the first extension 405A and the secondextension 405B to have rounded shapes after the second nanogap 114 iscut as shown in FIGS. 4C and 4D. The nanowire 106 is tapered in orderfor the first extension 405A and the second extension 405B to havetriangular shapes after the second nanogap 114 is cut as shown in FIG.4E.

The second nanogap 114 is formed by (i.e., is in between) the firstextension 405A and the second extension 405B. The size (e.g., thedistance X of the extensions 405A and 405B) of the second nanogap 114accommodates a single base or a single nucleotide of the target molecule511 in which the target molecule 511 may include a deoxyribonucleic acidmolecule, a ribonucleic acid molecule, and/or a protein that is to besequenced in the system 500. The size of the second nanogap 114 allows(only) the single base or the single nucleotide to be sequenced via ameasured current (of ammeter 520) while in the second nanogap 114between the first and second extensions.

The first extension 405A and the second extension 405B both extend intothe first nanogap 112.

FIG. 8 illustrates an example of a computer 800 (e.g., as part of thecomputer test setup for testing and analysis) which may implement,control, and/or regulate the respective voltages of the voltage sources,respective measurements of the ammeters, and display screens fordisplaying various current amplitude (including ionic current andtransistor (source to drain current)) as discussed herein. The computer800 also stores the respective electrical current amplitudes of eachbase tested and measured to be compared against the baselines currentamplitudes of different bases, which is utilized to identify the basesof the tested/target molecule.

Various methods, procedures, modules, flow diagrams, tools,applications, circuits, elements, and techniques discussed herein mayalso incorporate and/or utilize the capabilities of the computer 800.Moreover, capabilities of the computer 800 may be utilized to implementfeatures of exemplary embodiments discussed herein. One or more of thecapabilities of the computer 800 may be utilized to implement, toconnect to, and/or to support any element discussed herein (asunderstood by one skilled in the art) in FIGS. 1-7. For example, thecomputer 800 which may be any type of computing device and/or testequipment (including ammeters, voltage sources, current meters,connectors, etc.). Input/output device 870 (having proper software andhardware) of computer 800 may include and/or be coupled to thenanodevices and structures discussed herein via cables, plugs, wires,electrodes, patch clamps, etc. Also, the communication interface of theinput/output devices 870 comprises hardware and software forcommunicating with, operatively connecting to, reading, and/orcontrolling voltage sources, ammeters, and current traces (e.g.,magnitude and time duration of current), etc., as discussed andunderstood herein. The user interfaces of the input/output device 870may include, e.g., a track ball, mouse, pointing device, keyboard, touchscreen, etc., for interacting with the computer 800, such as inputtinginformation, making selections, independently controlling differentvoltages sources, and/or displaying, viewing and recording currenttraces for each base, molecule, biomolecules, etc.

Generally, in terms of hardware architecture, the computer 800 mayinclude one or more processors 810, computer readable storage memory820, and one or more input and/or output (I/O) devices 870 that arecommunicatively coupled via a local interface (not shown). The localinterface can be, for example but not limited to, one or more buses orother wired or wireless connections, as is known in the art. The localinterface may have additional elements, such as controllers, buffers(caches), drivers, repeaters, and receivers, to enable communications.Further, the local interface may include address, control, and/or dataconnections to enable appropriate communications among theaforementioned components.

The processor 810 is a hardware device for executing software that canbe stored in the memory 820. The processor 810 can be virtually anycustom made or commercially available processor, a central processingunit (CPU), a data signal processor (DSP), or an auxiliary processoramong several processors associated with the computer 800, and theprocessor 810 may be a semiconductor based microprocessor (in the formof a microchip) or a macroprocessor.

The computer readable memory 820 can include any one or combination ofvolatile memory elements (e.g., random access memory (RAM), such asdynamic random access memory (DRAM), static random access memory (SRAM),etc.) and nonvolatile memory elements (e.g., ROM, erasable programmableread only memory (EPROM), electronically erasable programmable read onlymemory (EEPROM), programmable read only memory (PROM), tape, compactdisc read only memory (CD-ROM), disk, diskette, cartridge, cassette orthe like, etc.). Moreover, the memory 820 may incorporate electronic,magnetic, optical, and/or other types of storage media. Note that thememory 820 can have a distributed architecture, where various componentsare situated remote from one another, but can be accessed by theprocessor 810.

The software in the computer readable memory 820 may include one or moreseparate programs, each of which comprises an ordered listing ofexecutable instructions for implementing logical functions. The softwarein the memory 820 includes a suitable operating system (O/S) 850,compiler 840, source code 830, and one or more applications 860 of theexemplary embodiments. As illustrated, the application 860 comprisesnumerous functional components for implementing the features, processes,methods, functions, and operations of the exemplary embodiments.

The operating system 850 may control the execution of other computerprograms, and provides scheduling, input-output control, file and datamanagement, memory management, and communication control and relatedservices.

The application 860 may be a source program, executable program (objectcode), script, or any other entity comprising a set of instructions tobe performed. When a source program, then the program is usuallytranslated via a compiler (such as the compiler 840), assembler,interpreter, or the like, which may or may not be included within thememory 820, so as to operate properly in connection with the O/S 850.Furthermore, the application 860 can be written as (a) an objectoriented programming language, which has classes of data and methods, or(b) a procedure programming language, which has routines, subroutines,and/or functions.

The I/O devices 870 may include input devices (or peripherals) such as,for example but not limited to, a mouse, keyboard, scanner, microphone,camera, etc. Furthermore, the I/O devices 870 may also include outputdevices (or peripherals), for example but not limited to, a printer,display, etc. Finally, the I/O devices 870 may further include devicesthat communicate both inputs and outputs, for instance but not limitedto, a NIC or modulator/demodulator (for accessing remote devices, otherfiles, devices, systems, or a network), a radio frequency (RF) or othertransceiver, a telephonic interface, a bridge, a router, etc. The I/Odevices 870 also include components for communicating over variousnetworks, such as the Internet or an intranet. The I/O devices 870 maybe connected to and/or communicate with the processor 810 utilizingBluetooth connections and cables (via, e.g., Universal Serial Bus (USB)ports, serial ports, parallel ports, FireWire, HDMI (High-DefinitionMultimedia Interface), etc.).

In exemplary embodiments, where the application 860 is implemented inhardware, the application 860 can be implemented with any one or acombination of the following technologies, which are each well known inthe art: a discrete logic circuit(s) having logic gates for implementinglogic functions upon data signals, an application specific integratedcircuit (ASIC) having appropriate combinational logic gates, aprogrammable gate array(s) (PGA), a field programmable gate array(FPGA), etc.

As will be appreciated by one skilled in the art, aspects of the presentinvention may be embodied as a system, method or computer programproduct. Accordingly, aspects of the present invention may take the formof an entirely hardware embodiment, an entirely software embodiment(including firmware, resident software, micro-code, etc.) or anembodiment combining software and hardware aspects that may allgenerally be referred to herein as a “circuit,” “module” or “system.”Furthermore, aspects of the present invention may take the form of acomputer program product embodied in one or more computer readablemedium(s) having computer readable program code embodied thereon.

Any combination of one or more computer readable medium(s) may beutilized. The computer readable medium may be a computer readable signalmedium or a computer readable storage medium. A computer readablestorage medium may be, for example, but not limited to, an electronic,magnetic, optical, electromagnetic, infrared, or semiconductor system,apparatus, or device, or any suitable combination of the foregoing. Morespecific examples (a non-exhaustive list) of the computer readablestorage medium would include the following: an electrical connectionhaving one or more wires, a portable computer diskette, a hard disk, arandom access memory (RAM), a read-only memory (ROM), an erasableprogrammable read-only memory (EPROM or Flash memory), an optical fiber,a portable compact disc read-only memory (CD-ROM), an optical storagedevice, a magnetic storage device, or any suitable combination of theforegoing. In the context of this document, a computer readable storagemedium may be any tangible medium that can contain, or store a programfor use by or in connection with an instruction execution system,apparatus, or device.

A computer readable signal medium may include a propagated data signalwith computer readable program code embodied therein, for example, inbaseband or as part of a carrier wave. Such a propagated signal may takeany of a variety of forms, including, but not limited to,electro-magnetic, optical, or any suitable combination thereof. Acomputer readable signal medium may be any computer readable medium thatis not a computer readable storage medium and that can communicate,propagate, or transport a program for use by or in connection with aninstruction execution system, apparatus, or device.

Program code embodied on a computer readable medium may be transmittedusing any appropriate medium, including but not limited to wireless,wireline, optical fiber cable, RF, etc., or any suitable combination ofthe foregoing.

Computer program code for carrying out operations for aspects of thepresent invention may be written in any combination of one or moreprogramming languages, including an object oriented programming languagesuch as Java, Smalltalk, C++ or the like and conventional proceduralprogramming languages, such as the “C” programming language or similarprogramming languages. The program code may execute entirely on theuser's computer, partly on the user's computer, as a stand-alonesoftware package, partly on the user's computer and partly on a remotecomputer or entirely on the remote computer or server. In the latterscenario, the remote computer may be connected to the user's computerthrough any type of network, including a local area network (LAN) or awide area network (WAN), or the connection may be made to an externalcomputer (for example, through the Internet using an Internet ServiceProvider).

Aspects of the present invention are described below with reference toflowchart illustrations and/or block diagrams of methods, apparatus(systems) and computer program products according to embodiments of theinvention. It will be understood that each block of the flowchartillustrations and/or block diagrams, and combinations of blocks in theflowchart illustrations and/or block diagrams, can be implemented bycomputer program instructions. These computer program instructions maybe provided to a processor of a general purpose computer, specialpurpose computer, or other programmable data processing apparatus toproduce a machine, such that the instructions, which execute via theprocessor of the computer or other programmable data processingapparatus, create means for implementing the functions/acts specified inthe flowchart and/or block diagram block or blocks.

These computer program instructions may also be stored in a computerreadable medium that can direct a computer, other programmable dataprocessing apparatus, or other devices to function in a particularmanner, such that the instructions stored in the computer readablemedium produce an article of manufacture including instructions whichimplement the function/act specified in the flowchart and/or blockdiagram block or blocks.

The computer program instructions may also be loaded onto a computer,other programmable data processing apparatus, or other devices to causea series of operational steps to be performed on the computer, otherprogrammable apparatus or other devices to produce a computerimplemented process such that the instructions which execute on thecomputer or other programmable apparatus provide processes forimplementing the functions/acts specified in the flowchart and/or blockdiagram block or blocks.

The flowchart and block diagrams in the Figures illustrate thearchitecture, functionality, and operation of possible implementationsof systems, methods and computer program products according to variousembodiments of the present invention. In this regard, each block in theflowchart or block diagrams may represent a module, segment, or portionof code, which comprises one or more executable instructions forimplementing the specified logical function(s). It should also be notedthat, in some alternative implementations, the functions noted in theblock may occur out of the order noted in the figures. For example, twoblocks shown in succession may, in fact, be executed substantiallyconcurrently, or the blocks may sometimes be executed in the reverseorder, depending upon the functionality involved. It will also be notedthat each block of the block diagrams and/or flowchart illustration, andcombinations of blocks in the block diagrams and/or flowchartillustration, can be implemented by special purpose hardware-basedsystems that perform the specified functions or acts, or combinations ofspecial purpose hardware and computer instructions.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. It will be further understood that the terms “comprises”and/or “comprising,” when used in this specification, specify thepresence of stated features, integers, steps, operations, elements,and/or components, but do not preclude the presence or addition of onemore other features, integers, steps, operations, element components,and/or groups thereof.

The corresponding structures, materials, acts, and equivalents of allmeans or step plus function elements in the claims below are intended toinclude any structure, material, or act for performing the function incombination with other claimed elements as specifically claimed. Thedescription of the present invention has been presented for purposes ofillustration and description, but is not intended to be exhaustive orlimited to the invention in the form disclosed. Many modifications andvariations will be apparent to those of ordinary skill in the artwithout departing from the scope and spirit of the invention. Theembodiment was chosen and described in order to best explain theprinciples of the invention and the practical application, and to enableothers of ordinary skill in the art to understand the invention forvarious embodiments with various modifications as are suited to theparticular use contemplated

The flow diagrams depicted herein are just one example. There may bemany variations to this diagram or the steps (or operations) describedtherein without departing from the spirit of the invention. Forinstance, the steps may be performed in a differing order or steps maybe added, deleted or modified. All of these variations are considered apart of the claimed invention.

While the preferred embodiment to the invention had been described, itwill be understood that those skilled in the art, both now and in thefuture, may make various improvements and enhancements which fall withinthe scope of the claims which follow. These claims should be construedto maintain the proper protection for the invention first described.

What is claimed is:
 1. A structure utilized in sequencing, the structure comprising: an oxide on a wafer; a nanowire on the oxide; a first nanowire part and a second nanowire part formed of the nanowire, wherein the first nanowire part and the second nanowire part are separate and directly opposite from one another to form a first nanogap; wherein the first nanowire part and the second nanowire part have straight portions opposing to and parallel to one another that form the first nanogap; wherein the first nanogap is defined between the straight portions of the first nanowire part and the second nanowire part; wherein the first nanogap ranges from 4 to 10 nanometers; a first extension attached to and extending from the straight portion of the first nanowire part; a second extension attached to and extending from the straight portion of the second nanowire part, wherein the first extension and the second extension extend toward each other; a second nanogap formed between the first extension and the second extension; wherein the second nanogap is structured for a target molecule to pass between the first extension and the second extension having formed the second nanogap.
 2. The structure of claim 1, wherein the second nanogap is thinner than the first nanogap.
 3. The structure of claim 1, wherein the nanowire is tapered in order for the first extension and the second extension to have rectangular shapes after the second nanogap is cut.
 4. The structure of claim 1, wherein the nanowire is tapered in order for the first extension and the second extension to have rounded shapes after the second nanogap is cut.
 5. The structure of claim 1, wherein the nanowire is tapered in order for the first extension and the second extension to have triangular shapes after the second nanogap is cut.
 6. The structure of claim 1, wherein the second nanogap is smaller than the first nanogap.
 7. The structure of claim 1, wherein the second nanogap ranges from 0.3 to 1 nanometer.
 8. The structure of claim 1, further comprising: a first reservoir; and a second reservoir, the second nanogap connecting the first reservoir to the second reservoir.
 9. The structure of claim 1, wherein the first extension of the first nanowire part is tapered; and wherein the second extension of the second nanowire part is tapered. 